Sorry if my question is a little silly, but i have the following problem.
I aligned some sequences from a family gene according to an specific domain of the protein. I`m not include the entire protein because the others domains are less conserved. In my work, I did annotations using Blast and Interproscan to confirm, besides confirm important motifs using MEME/MAST. I clustered the phylogenetic tree in order to observed relationships in this domain and cluster are well supported with bootstrapping values over 80% in the informative branches to me and in a many few of them over 68, that it was the minimum value obtained. When i look inside the clusters formed, the cluster show an identity values from 29 %. According to my work I think that the clustering its rigth, and I think despite of this values, if I can obtained the similarity values, i can support the cluster better, because i can say that this clusters are reflecting functional relationships, but i don't know how to obtained this values to report it. Can you help me? Please? the question is How can i obtained the similarity values among sequences in a multiple sequence alignment of protein sequences?
Protein Sequence Clusters